public class OmssaParameters extends Object implements IdentificationAlgorithmParameter
Constructor and Description |
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OmssaParameters()
Constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same
parameters.
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Advocate |
getAlgorithm()
Returns the identification algorithm.
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double |
getConsecutiveIonProbability()
Returns the consecutive ion probability.
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int |
getDoubleChargeWindow()
Returns the window size for doubly charged ions.
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double |
getFractionOfPeaksForChargeEstimation()
Returns the fraction of peaks to be retained for charge >1 estimation.
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double |
getHighIntensityCutOff()
Returns the high intensity cut-off as percentage of the most intense ion
peak.
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int |
getHitListLength()
Returns the length of the hit list for OMSSA.
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double |
getIntensityCutOffIncrement()
Returns the intensity cut-off increment.
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double |
getIterativeReplaceEvalue()
Returns the e-value threshold to use to replace a hit for the iterative
search.
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double |
getIterativeSequenceEvalue()
Returns the e-value threshold to use to consider a sequence for the
iterative search.
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double |
getIterativeSpectrumEvalue()
Returns the e-value threshold to use consider a spectrum for the
iterative search.
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double |
getLowIntensityCutOff()
Returns the low intensity cut-off as percentage of the most intense ion
peak.
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double |
getMaxEValue()
Returns the maximal e-value searched for.
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int |
getMaxFragmentCharge()
Returns the maximal fragment charge.
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int |
getMaxFragmentPerSeries()
Returns the maximal number of fragments to retain per series.
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int |
getMaxHitsPerSpectrumPerCharge()
Returns the maximal number of hits searched per spectrum and per charge.
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int |
getMaxMzLadders()
Returns the maximal m/z ladder length.
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int |
getMaxPeptideLength()
Returns the maximal peptide length allowed.
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int |
getMinAnnotatedPeaks()
Returns the minimal number of annotated peaks a peptide should have.
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int |
getMinimalChargeForMultipleChargedFragments()
Returns the minimal precursor charge to account for multiply charged
fragments in OMSSA.
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int |
getMinPeaks()
Returns the minimal number of peaks a spectrum should contain.
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int |
getMinPeptideLength()
Sets the minimal peptide length allowed.
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int |
getMinPrecPerSpectrum()
Returns the minimal number of precursors per spectrum.
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String |
getModificationName(int ptmIndex)
Returns the name of the modification indexed by the given index.
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int |
getnAnnotatedMostIntensePeaks()
Returns the minimal number of annotated most intense peaks.
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double |
getNeutronThreshold()
Returns the mass after which exact neutron mass should be considered in
the calculation.
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ArrayList<Integer> |
getNoProlineRuleSeries()
Returns the id numbers of ion series to apply no product ions at proline
rule at.
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int |
getnPeaksInDoubleChargeWindow()
Returns the number of peaks in doubly charged windows.
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int |
getnPeaksInSingleChargeWindow()
Returns the number of peaks in singly charged windows.
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static HashMap<String,Integer> |
getOMSSAIndexes(File modificationsFile)
Imports the OMSSA indexes from an XML file.
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static String[] |
getOmssaOutputTypes()
Returns the output types available.
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int |
getPtmIndex(String modificationName)
Returns the index of a given modification
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HashMap<Integer,String> |
getPtmIndexes()
Returns the PTM indexes as a map.
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String |
getSelectedOutput()
Returns the selected output type, omx, csv or pepXML.
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int |
getSingleChargeWindow()
Returns the window size for singly charged ions.
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boolean |
hasPtmIndexes()
Indicates whether the modification profile has PTM indexes.
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boolean |
isCleaveNterMethionine()
Indicates whether N-terminal methionines should be cleaved.
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boolean |
isDetermineChargePlusOneAlgorithmically()
Indicates whether charge plus one should be determined algorithmically.
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boolean |
isEstimateCharge()
Indicates whether the precursor charge shall be estimated for OMSSA.
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boolean |
isMemoryMappedSequenceLibraries()
Indicates whether sequence libraries should be mapped in memory.
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boolean |
isRemovePrecursor()
Indicates whether the precursor shall be removed for OMSSA.
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boolean |
isScalePrecursor()
Indicates whether the precursor shall be scaled for OMSSA.
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boolean |
isSearchForwardFragmentFirst()
Indicates whether forward ions (b1) should be searched first.
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boolean |
isSearchPositiveIons()
Indicates whether positive ions are searched.
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boolean |
isSearchRewindFragments()
Indicates whether C-terminal fragments should be searched.
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boolean |
isUseCorrelationCorrectionScore()
Indicates whether the correlation correction score should be used.
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void |
setCleaveNterMethionine(boolean cleaveNterMethionine)
Sets whether N-terminal methionines should be cleaved.
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void |
setConsecutiveIonProbability(double consecutiveIonProbability)
Set the consecutive ion probability.
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void |
setDetermineChargePlusOneAlgorithmically(boolean determineChargePlusOneAlgorithmically)
Sets whether charge plus one should be determined algorithmically.
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void |
setDoubleChargeWindow(int doubleChargeWindow)
Sets the window size for doubly charged ions.
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void |
setEstimateCharge(boolean estimateCharge)
Sets whether the precursor charge shall be estimated for OMSSA.
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void |
setFractionOfPeaksForChargeEstimation(double fractionOfPeaksForChargeEstimation)
Sets the fraction of peaks to be retained for charge >1 estimation.
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void |
setHighIntensityCutOff(double highIntensityCutOff)
Sets the high intensity cut-off as percentage of the most intense ion
peak.
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void |
setHitListLength(int hitListLength)
Sets the length of the hit list for OMSSA.
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void |
setIntensityCutOffIncrement(double intensityCutOffIncrement)
Sets the intensity cut-off increment.
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void |
setIterativeReplaceEvalue(double iterativeReplaceEvalue)
Sets the e-value threshold to use to replace a hit for the iterative
search.
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void |
setIterativeSequenceEvalue(double iterativeSequenceEvalue)
Sets the e-value threshold to use to consider a sequence for the
iterative search.
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void |
setIterativeSpectrumEvalue(double iterativeSpectrumEvalue)
Sets the e-value threshold to use consider a spectrum for the iterative
search.
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void |
setLowIntensityCutOff(double lowIntensityCutOff)
Sets the low intensity cut-off as percentage of the most intense ion
peak.
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void |
setMaxEValue(double maxEValue)
Sets the maximal e-value searched for.
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void |
setMaxFragmentCharge(int maxFragmentCharge)
Sets the maximal fragment charge.
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void |
setMaxFragmentPerSeries(int maxFragmentPerSeries)
Sets the maximal number of fragments to retain per series.
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void |
setMaxHitsPerSpectrumPerCharge(int maxHitsPerSpectrumPerCharge)
Set the maximal number of hits searched per spectrum and per charge.
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void |
setMaxMzLadders(int maxMzLadders)
Sets the maximal m/z ladder length.
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void |
setMaxPeptideLength(int maxPeptideLength)
Sets the maximal peptide length allowed.
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void |
setMemoryMappedSequenceLibraries(boolean memoryMappedSequenceLibraries)
Sets whether sequence libraries should be mapped in memory.
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void |
setMinAnnotatedPeaks(int minAnnotatedPeaks)
Sets the minimal number of annotated peaks a peptide should have.
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void |
setMinimalChargeForMultipleChargedFragments(int minimalChargeForMultipleChargedFragments)
Sets the minimal precursor charge to account for multiply charged
fragments in OMSSA.
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void |
setMinPeaks(int minPeaks)
Sets the minimal number of peaks a spectrum should contain.
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void |
setMinPeptideLength(int minPeptideLength)
Sets the minimal peptide length allowed.
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void |
setMinPrecPerSpectrum(int minPrecPerSpectrum)
Sets the minimal number of precursors per spectrum.
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void |
setnAnnotatedMostIntensePeaks(int nAnnotatedMostIntensePeaks)
Sets the minimal number of annotated most intense peaks.
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void |
setNeutronThreshold(double neutronThreshold)
Sets the mass after which exact neutron mass should be considered in the
calculation.
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void |
setNoProlineRuleSeries(ArrayList<Integer> noProlineRuleSeries)
Sets the id numbers of ion series to apply no product ions at proline
rule at.
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void |
setnPeaksInDoubleChargeWindow(int nPeaksIndoubleChargeWindow)
Sets the number of peaks in doubly charged windows.
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void |
setnPeaksInSingleChargeWindow(int nPeaksInSingleChargeWindow)
Sets the number of peaks in singly charged windows.
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void |
setPtmIndex(String modificationName,
int ptmIndex)
Sets the index for a given modification.
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void |
setPtmIndexes(ModificationParameters modificationProfile)
Set the PTM indexes of the modifications searched.
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void |
setRemovePrecursor(boolean removePrecursor)
Sets whether the precursor shall be removed for OMSSA.
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void |
setScalePrecursor(boolean scalePrecursor)
Sets whether the precursor shall be scaled for OMSSA.
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void |
setSearchForwardFragmentFirst(boolean searchForwardFragmentFirst)
Sets whether forward ions (b1) should be searched first.
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void |
setSearchPositiveIons(boolean searchPositiveIons)
Sets whether positive ions are searched.
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void |
setSearchRewindFragments(boolean searchRewindFragments)
Sets whether C-terminal fragments should be searched.
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void |
setSelectedOutput(String selectedOutput)
Sets the output type, omx, csv or pepXML.
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void |
setSingleChargeWindow(int singleChargeWindow)
Sets the window size for singly charged ions.
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void |
setUseCorrelationCorrectionScore(boolean useCorrelationCorrectionScore)
Sets whether the correlation correction score should be used.
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String |
toString(boolean html)
Returns the parameters as a string.
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public double getMaxEValue()
public void setMaxEValue(double maxEValue)
maxEValue
- the maximal e-value searched forpublic int getHitListLength()
public void setHitListLength(int hitListLength)
hitListLength
- the length of the hit list for OMSSApublic int getMinimalChargeForMultipleChargedFragments()
public void setMinimalChargeForMultipleChargedFragments(int minimalChargeForMultipleChargedFragments)
minimalChargeForMultipleChargedFragments
- the minimal precursor
charge to account for multiply charged fragments in OMSSApublic int getMaxPeptideLength()
public void setMaxPeptideLength(int maxPeptideLength)
maxPeptideLength
- the maximal peptide length allowedpublic int getMinPeptideLength()
public void setMinPeptideLength(int minPeptideLength)
minPeptideLength
- the minimal peptide length allowedpublic boolean isEstimateCharge()
public void setEstimateCharge(boolean estimateCharge)
estimateCharge
- a boolean indicating whether the precursor charge
shall be estimated for OMSSApublic boolean isRemovePrecursor()
public void setRemovePrecursor(boolean removePrecursor)
removePrecursor
- a boolean indicating whether the precursor shall
be removed for OMSSApublic boolean isScalePrecursor()
public void setScalePrecursor(boolean scalePrecursor)
scalePrecursor
- a boolean indicating whether the precursor shall be
scaled for OMSSApublic String getSelectedOutput()
public void setSelectedOutput(String selectedOutput)
selectedOutput
- the output typepublic static String[] getOmssaOutputTypes()
public boolean isMemoryMappedSequenceLibraries()
public void setMemoryMappedSequenceLibraries(boolean memoryMappedSequenceLibraries)
memoryMappedSequenceLibraries
- a boolean indicating whether
sequence libraries should be mapped in memorypublic double getNeutronThreshold()
public void setNeutronThreshold(double neutronThreshold)
neutronThreshold
- the mass after which exact neutron mass should be
considered in the calculationpublic double getLowIntensityCutOff()
public void setLowIntensityCutOff(double lowIntensityCutOff)
lowIntensityCutOff
- the low intensity cut-off as percentage of the
most intense ion peakpublic double getHighIntensityCutOff()
public void setHighIntensityCutOff(double highIntensityCutOff)
highIntensityCutOff
- the high intensity cut-off as percentage of
the most intense ion peakpublic double getIntensityCutOffIncrement()
public void setIntensityCutOffIncrement(double intensityCutOffIncrement)
intensityCutOffIncrement
- the intensity cut-off incrementpublic int getSingleChargeWindow()
public void setSingleChargeWindow(int singleChargeWindow)
singleChargeWindow
- the window size for singly charged ionspublic int getDoubleChargeWindow()
public void setDoubleChargeWindow(int doubleChargeWindow)
doubleChargeWindow
- the window size for doubly charged ionspublic int getnPeaksInSingleChargeWindow()
public void setnPeaksInSingleChargeWindow(int nPeaksInSingleChargeWindow)
nPeaksInSingleChargeWindow
- the number of peaks in singly charged
windowspublic int getnPeaksInDoubleChargeWindow()
public void setnPeaksInDoubleChargeWindow(int nPeaksIndoubleChargeWindow)
nPeaksIndoubleChargeWindow
- the number of peaks in doubly charged
windowspublic int getMaxHitsPerSpectrumPerCharge()
public void setMaxHitsPerSpectrumPerCharge(int maxHitsPerSpectrumPerCharge)
maxHitsPerSpectrumPerCharge
- the maximal number of hits searched
per spectrum and per chargepublic int getnAnnotatedMostIntensePeaks()
public void setnAnnotatedMostIntensePeaks(int nAnnotatedMostIntensePeaks)
nAnnotatedMostIntensePeaks
- the minimal number of annotated most
intense peakspublic int getMinAnnotatedPeaks()
public void setMinAnnotatedPeaks(int minAnnotatedPeaks)
minAnnotatedPeaks
- the minimal number of annotated peaks a peptide
should havepublic int getMinPeaks()
public void setMinPeaks(int minPeaks)
minPeaks
- the minimal number of peaks a spectrum should containpublic boolean isCleaveNterMethionine()
public void setCleaveNterMethionine(boolean cleaveNterMethionine)
cleaveNterMethionine
- whether N-terminal methionines should be
cleavedpublic int getMaxMzLadders()
public void setMaxMzLadders(int maxMzLadders)
maxMzLadders
- the maximal m/z ladder lengthpublic int getMaxFragmentCharge()
public void setMaxFragmentCharge(int maxFragmentCharge)
maxFragmentCharge
- the maximal fragment chargepublic double getFractionOfPeaksForChargeEstimation()
public void setFractionOfPeaksForChargeEstimation(double fractionOfPeaksForChargeEstimation)
fractionOfPeaksForChargeEstimation
- the fraction of peaks to be
retained for charge >1 estimationpublic boolean isDetermineChargePlusOneAlgorithmically()
public void setDetermineChargePlusOneAlgorithmically(boolean determineChargePlusOneAlgorithmically)
determineChargePlusOneAlgorithmically
- whether charge plus one
should be determined algorithmicallypublic boolean isSearchPositiveIons()
public void setSearchPositiveIons(boolean searchPositiveIons)
searchPositiveIons
- a boolean indicating whether positive ions are
searchedpublic int getMinPrecPerSpectrum()
public void setMinPrecPerSpectrum(int minPrecPerSpectrum)
minPrecPerSpectrum
- the minimal number of precursors per spectrumpublic boolean isSearchForwardFragmentFirst()
public void setSearchForwardFragmentFirst(boolean searchForwardFragmentFirst)
searchForwardFragmentFirst
- whether forward ions (b1) should be
searched firstpublic boolean isSearchRewindFragments()
public void setSearchRewindFragments(boolean searchRewindFragments)
searchRewindFragments
- whether C-terminal fragments should be
searchedpublic int getMaxFragmentPerSeries()
public void setMaxFragmentPerSeries(int maxFragmentPerSeries)
maxFragmentPerSeries
- the maximal number of fragments to retain per
seriespublic boolean isUseCorrelationCorrectionScore()
public void setUseCorrelationCorrectionScore(boolean useCorrelationCorrectionScore)
useCorrelationCorrectionScore
- a boolean indicating whether the
correlation correction score should be usedpublic double getConsecutiveIonProbability()
public void setConsecutiveIonProbability(double consecutiveIonProbability)
consecutiveIonProbability
- the consecutive ion probabilitypublic double getIterativeSequenceEvalue()
public void setIterativeSequenceEvalue(double iterativeSequenceEvalue)
iterativeSequenceEvalue
- the e-value threshold to use to consider a
sequence for the iterative searchpublic double getIterativeReplaceEvalue()
public void setIterativeReplaceEvalue(double iterativeReplaceEvalue)
iterativeReplaceEvalue
- the e-value threshold to use to replace a
hit for the iterative searchpublic double getIterativeSpectrumEvalue()
public void setIterativeSpectrumEvalue(double iterativeSpectrumEvalue)
iterativeSpectrumEvalue
- the e-value threshold to use consider a
spectrum for the iterative searchpublic ArrayList<Integer> getNoProlineRuleSeries()
public void setNoProlineRuleSeries(ArrayList<Integer> noProlineRuleSeries)
noProlineRuleSeries
- the id numbers of ion series to apply no
product ions at proline rule atpublic void setPtmIndex(String modificationName, int ptmIndex)
modificationName
- the name of the modificationptmIndex
- the index of the modificationpublic String getModificationName(int ptmIndex)
ptmIndex
- the index of the modification to look forpublic boolean hasPtmIndexes()
public int getPtmIndex(String modificationName)
modificationName
- the name of the modificationpublic HashMap<Integer,String> getPtmIndexes()
public void setPtmIndexes(ModificationParameters modificationProfile)
modificationProfile
- the modification profile of this searchpublic static HashMap<String,Integer> getOMSSAIndexes(File modificationsFile) throws org.xmlpull.v1.XmlPullParserException, FileNotFoundException, IOException
modificationsFile
- the modification fileorg.xmlpull.v1.XmlPullParserException
- if an XmlPullParserException occursFileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occurspublic Advocate getAlgorithm()
IdentificationAlgorithmParameter
getAlgorithm
in interface IdentificationAlgorithmParameter
public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
IdentificationAlgorithmParameter
equals
in interface IdentificationAlgorithmParameter
identificationAlgorithmParameter
- the other
identificationAlgorithmParameterpublic String toString(boolean html)
IdentificationAlgorithmParameter
toString
in interface IdentificationAlgorithmParameter
html
- use HTML formattingCopyright © 2018. All rights reserved.